3D Print Toolbox Intersection Check Problems
This is a real regression indeed, compared e.g. to version 2.83.4. I see you've also asked here: https://blenderartists.org/t/strange-results-using-3d-print-toolbox-to-check-intersections/1258126 (pasting to ensure others can find an answer if it's posted there).
The only solution for now is to keep the 2.8x version around and use it primarily for running the 3D analysis, then moving up to 2.90.1. I have no other solution for now.
Is the issue reported on the blender bug tracker? Given importance of 3D printing and such, I would think Blender can afford an auto test ensuring such regressions does not slip between stable versions.
Cheers.